List of works - Peter M Kasson

"Cross-graining": efficient multi-scale simulation via Markov state models.

scientific article published in January 2010

A bundling of viral fusion mechanisms

scientific article

A hybrid machine-learning approach for segmentation of protein localization data

scientific article

Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics

scientific article published on 25 October 2019

Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails

scientific article

Computational biology in the cloud: methods and new insights from computing at scale.

scientific article published in January 2013

Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics

scientific article

Coupled diffusion in lipid bilayers upon close approach.

scientific article

Deformable modeling for improved calculation of molecular velocities from single-particle tracking.

scientific article published in January 2005

Disentangling Viral Membrane Fusion from Receptor Binding Using Synthetic DNA-Lipid Conjugates

scientific article

Dynamic heterogeneity controls diffusion and viscosity near biological interfaces

scientific article

Ebolavirus entry requires a compact hydrophobic fist at the tip of the fusion loop

scientific article

Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

scholarly article

Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance

scientific article

Formation of a highly peptide-receptive state of class II MHC.

scientific article published in November 1998

Function and dynamics of macromolecular complexes explored by integrative structural and computational biology

scientific article published in August 2014

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

scientific article

Hemagglutinin Spatial Distribution Shifts in Response to Cholesterol in the Influenza Viral Envelope

scientific article

Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data

scientific article published on 07 June 2019

Improving pandemic influenza risk assessment

scientific article

Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion

scientific article published on 16 January 2018

Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms

scientific article published on 18 March 2020

Influenza viral membrane fusion is sensitive to sterol concentration but surprisingly robust to sterol chemical identity

scientific article

Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity

scientific article published on 15 April 2020

Lipid converter, a framework for lipid manipulations in molecular dynamics simulations

scientific article

Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models

scientific article

Model for a novel membrane envelope in a filamentous hyperthermophilic virus

scientific article published on 22 June 2017

Molecular dynamics simulation of lipid reorientation at bilayer edges.

scientific article

Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform

scientific article

Multiphasic effects of cholesterol on influenza fusion kinetics reflect multiple mechanistic roles

scientific article

Persistent voids: a new structural metric for membrane fusion.

scientific article

Precise triggering and chemical control of single-virus fusion within endosomes

scientific article published on 28 October 2020

Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme

scientific article published on 19 July 2017

Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.

scientific article

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions

scientific article

Quantitative imaging of lymphocyte membrane protein reorganization and signaling

scientific article

Receptor binding by influenza virus: using computational techniques to extend structural data

scientific article

Refinement of highly flexible protein structures using simulation-guided spectroscopy

scientific article published on 27 November 2018

Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin.

scientific article

Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile

scientific article published in Nature Communications

Structure of the Neisserial outer membrane protein Opa₆₀: loop flexibility essential to receptor recognition and bacterial engulfment

scientific article

Viral factors in influenza pandemic risk assessment.

scientific article

Water ordering at membrane interfaces controls fusion dynamics

scientific article

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

scientific article published on 14 February 2022

List of works by Peter M Kasson

"Cross-graining": efficient multi-scale simulation via Markov state models.

A bundling of viral fusion mechanisms

A hybrid machine-learning approach for segmentation of protein localization data

Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics

Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails

Computational biology in the cloud: methods and new insights from computing at scale.

Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics

Coupled diffusion in lipid bilayers upon close approach.

Deformable modeling for improved calculation of molecular velocities from single-particle tracking.

Disentangling Viral Membrane Fusion from Receptor Binding Using Synthetic DNA-Lipid Conjugates

Dynamic heterogeneity controls diffusion and viscosity near biological interfaces

Ebolavirus entry requires a compact hydrophobic fist at the tip of the fusion loop

Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance

Formation of a highly peptide-receptive state of class II MHC.

Function and dynamics of macromolecular complexes explored by integrative structural and computational biology

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Hemagglutinin Spatial Distribution Shifts in Response to Cholesterol in the Influenza Viral Envelope

Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data

Improving pandemic influenza risk assessment

Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion

Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms

Influenza viral membrane fusion is sensitive to sterol concentration but surprisingly robust to sterol chemical identity

Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity

Lipid converter, a framework for lipid manipulations in molecular dynamics simulations

Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models

Model for a novel membrane envelope in a filamentous hyperthermophilic virus

Molecular dynamics simulation of lipid reorientation at bilayer edges.

Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform

Multiphasic effects of cholesterol on influenza fusion kinetics reflect multiple mechanistic roles

Persistent voids: a new structural metric for membrane fusion.

Precise triggering and chemical control of single-virus fusion within endosomes

Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme

Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions

Quantitative imaging of lymphocyte membrane protein reorganization and signaling

Receptor binding by influenza virus: using computational techniques to extend structural data

Refinement of highly flexible protein structures using simulation-guided spectroscopy

Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin.

Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile

Structure of the Neisserial outer membrane protein Opa₆₀: loop flexibility essential to receptor recognition and bacterial engulfment

Viral factors in influenza pandemic risk assessment.

Water ordering at membrane interfaces controls fusion dynamics

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support